CAD geometries are most often exchanged between analysis tools using NURBS patches to represent the boundary (BRep). We present a method where the control points of the BRep are used to automatically derive parametrisations suitable for shape optimisation with gradient-based methods. Particular focus is on ensuring geometric continuity between the NURBS patches, which is achieved through formulation of discrete constraints. Design variables then arise from formulating an orthogonal basis to the remaining design space using a singular value decomposition (SVD). The manuscript presents the extension of earlier work on B-spline surfaces to full NURBS surfaces and investigates the effect of the cutoff threshold of the SVD on the optimisation results. To enable routine automatic use, an estimation of the effective rank is proposed which allows to automatically determine the suitable cutoff threshold. The effectiveness of the algorithm is demonstrated for the minimisation of total pressure loss over a section of an automotive climate duct, and a U-bend cooling channel.